PBSIM: PacBio reads simulator--toward accurate genome assembly von Ono, Yukiteru, Asai, Kiyoshi, Hamada, Michiaki

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Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility von Terai, Goro, Asai, Kiyoshi

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ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures von Tagashira, Masaki, Asai, Kiyoshi

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Prediction of RNA secondary structure using generalized centroid estimators von Hamada, Michiaki, Kiryu, Hisanori, Sato, Kengo, Mituyama, Toutai, Asai, Kiyoshi

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Comprehensive prediction of lncRNA-RNA interactions in human transcriptome von Terai, Goro, Iwakiri, Junichi, Kameda, Tomoshi, Hamada, Michiaki, Asai, Kiyoshi

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m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing von Ninomiya, Kensuke, Iwakiri, Junichi, Aly, Mahmoud Khamis, Sakaguchi, Yuriko, Adachi, Shungo, Natsume, Tohru, Terai, Goro, Asai, Kiyoshi, Suzuki, Tsutomu, Hirose, Tetsuro

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RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp von Takizawa, Hiroki, Iwakiri, Junichi, Asai, Kiyoshi

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PBSIM3: a simulator for all types of PacBio and ONT long reads von Ono, Yukiteru, Hamada, Michiaki, Asai, Kiyoshi

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Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens von Tsukui, Takahiro, Nagano, Nozomi, Umemura, Myco, Kumagai, Toshitaka, Terai, Goro, Machida, Masayuki, Asai, Kiyoshi

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regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila von Saito, Kuniaki, Inagaki, Sachi, Mituyama, Toutai, Kawamura, Yoshinori, Ono, Yukiteru, Sakota, Eri, Kotani, Hazuki, Asai, Kiyoshi, Siomi, Haruhiko, Siomi, Mikiko C

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Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing von Iwakiri, Junichi, Tanaka, Kumiko, Chujo, Takeshi, Takakuwa, Hiro, Yamazaki, Tomohiro, Terai, Goro, Asai, Kiyoshi, Hirose, Tetsuro

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A fast structural multiple alignment method for long RNA sequences von Tabei, Yasuo, Kiryu, Hisanori, Kin, Taishin, Asai, Kiyoshi

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COSMO: A dynamic programming algorithm for multicriteria codon optimization von Taneda, Akito, Asai, Kiyoshi

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DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells von Shinriki, Satoru, Hirayama, Mayumi, Nagamachi, Akiko, Yokoyama, Akihiko, Kawamura, Takeshi, Kanai, Akinori, Kawai, Hidehiko, Iwakiri, Junichi, Liu, Rin, Maeshiro, Manabu, Tungalag, Saruul, Tasaki, Masayoshi, Ueda, Mitsuharu, Tomizawa, Kazuhito, Kataoka, Naoyuki, Ideue, Takashi, Suzuki, Yutaka, Asai, Kiyoshi, Tani, Tokio, Inaba, Toshiya, Matsui, Hirotaka

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Transformations for the compression of FASTQ quality scores of next-generation sequencing data von WAN, Raymond, VO NGOC ANH, ASAI, Kiyoshi

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Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities von Hagio, Taichi, Sakuraba, Shun, Iwakiri, Junichi, Mori, Ryota, Asai, Kiyoshi

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MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data von Umemura, Myco, Koike, Hideaki, Nagano, Nozomi, Ishii, Tomoko, Kawano, Jin, Yamane, Noriko, Kozone, Ikuko, Horimoto, Katsuhisa, Shin-ya, Kazuo, Asai, Kiyoshi, Yu, Jiujiang, Bennett, Joan W, Machida, Masayuki, Han, Kap-Hoon

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Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: application to sequenced genomes of Aspergillus and ten other filamentous fungal spe... von Takeda, Itaru, Umemura, Myco, Koike, Hideaki, Asai, Kiyoshi, Machida, Masayuki

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Improving the accuracy of predicting secondary structure for aligned RNA sequences von Hamada, Michiaki, Sato, Kengo, Asai, Kiyoshi

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Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations von Sakuraba, Shun, Asai, Kiyoshi, Kameda, Tomoshi

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